diff --git a/src/sentry/issues/ownership/grammar.py b/src/sentry/issues/ownership/grammar.py
index f7baedb2238a..7249c9a781a3 100644
--- a/src/sentry/issues/ownership/grammar.py
+++ b/src/sentry/issues/ownership/grammar.py
@@ -51,6 +51,7 @@ class OwnershipRule(TypedDict):
 PATH = "path"
 MODULE = "module"
 CODEOWNERS = "codeowners"
+EMPTY_CODEOWNERS_MATCHER = re.compile(rf"^\s*{CODEOWNERS}:\s*(?:#.*)?$")
 
 # Grammar is defined in EBNF syntax.
 ownership_grammar = Grammar(
@@ -327,6 +328,14 @@ def parse_rules(data: str) -> Any:
     return OwnershipVisitor().visit(tree)
 
 
+def remove_empty_codeowners_matchers(data: str) -> str:
+    return "".join(
+        line
+        for line in data.splitlines(keepends=True)
+        if not EMPTY_CODEOWNERS_MATCHER.match(line)
+    )
+
+
 def dump_schema(rules: Sequence[Rule]) -> OwnershipSchema:
     """Convert a Rule tree into a JSON schema"""
     return {"$version": VERSION, "rules": [r.dump() for r in rules]}
@@ -461,6 +470,9 @@ def convert_codeowners_syntax(
         else:
             formatted_path = path
 
+        if not formatted_path:
+            formatted_path = "/"
+
         if not code_owners:
             # Exclusion rule: path with no owners means "no ownership" for this path
             result += f"codeowners:{formatted_path}\n"
@@ -620,6 +632,8 @@ def create_schema_from_issue_owners(
     if issue_owners is None:
         return None
 
+    issue_owners = remove_empty_codeowners_matchers(issue_owners)
+
     try:
         rules = parse_rules(issue_owners)
     except ParseError as e:
diff --git a/tests/sentry/issues/ownership/test_grammar.py b/tests/sentry/issues/ownership/test_grammar.py
index 90d508433c11..552996ea2422 100644
--- a/tests/sentry/issues/ownership/test_grammar.py
+++ b/tests/sentry/issues/ownership/test_grammar.py
@@ -9,6 +9,7 @@
     Rule,
     convert_codeowners_syntax,
     convert_schema_to_rules_text,
+    create_schema_from_issue_owners,
     dump_schema,
     get_invalid_owner_details,
     load_schema,
@@ -1422,6 +1423,43 @@ def test_convert_codeowners_syntax_exclusion_with_stack_root() -> None:
     assert "codeowners:webpack://static/apps/github\n" in result
 
 
+def test_convert_codeowners_syntax_preserves_mapped_root_path() -> None:
+    code_mapping = type("", (), {})()
+    code_mapping.stack_root = ""
+    code_mapping.source_root = "/apps"
+
+    result = convert_codeowners_syntax(
+        "/apps @octocat\n",
+        {"@octocat": "octocat@sentry.io"},
+        code_mapping,
+    )
+    assert result == "codeowners:/ octocat@sentry.io\n"
+
+
+def test_convert_codeowners_syntax_preserves_mapped_root_exclusion() -> None:
+    code_mapping = type("", (), {})()
+    code_mapping.stack_root = ""
+    code_mapping.source_root = "/apps"
+
+    result = convert_codeowners_syntax(
+        "/apps\n",
+        {},
+        code_mapping,
+    )
+    assert result == "codeowners:/\n"
+
+
+def test_create_schema_from_issue_owners_skips_empty_codeowners_matcher() -> None:
+    assert (
+        create_schema_from_issue_owners(
+            project_id=1,
+            issue_owners="codeowners: #discover\n",
+            remove_deleted_owners=True,
+        )
+        == {"$version": 1, "rules": []}
+    )
+
+
 def test_parse_code_owners_exclusion_rule() -> None:
     codeowners = "/apps/ @getsentry/frontend\n/apps/github\n"
     teams, usernames, emails = parse_code_owners(codeowners)
diff --git a/tests/sentry/tasks/test_code_owners.py b/tests/sentry/tasks/test_code_owners.py
index bb37f518e0c1..2d9f618bd3c4 100644
--- a/tests/sentry/tasks/test_code_owners.py
+++ b/tests/sentry/tasks/test_code_owners.py
@@ -87,6 +87,32 @@ def test_simple(self) -> None:
         assert code_owners.schema == {"$version": 1, "rules": []}
         assert code_owners.date_synced is None
 
+    def test_update_schema_with_codeowners_root_mapping(self) -> None:
+        self.code_mapping.source_root = "/docs"
+        self.code_mapping.stack_root = ""
+        self.code_mapping.save()
+        self.code_owners.raw = "/docs @getsentry/ecosystem\n"
+        self.code_owners.save()
+
+        with self.tasks() and self.feature({"organizations:integrations-codeowners": True}):
+            self.create_external_team(integration=self.integration)
+            update_code_owners_schema(
+                organization=self.organization.id, integration=self.integration.id
+            )
+
+        code_owners = ProjectCodeOwners.objects.get(id=self.code_owners.id)
+        assert code_owners.schema == {
+            "$version": 1,
+            "rules": [
+                {
+                    "matcher": {"type": "codeowners", "pattern": "/"},
+                    "owners": [
+                        {"type": "team", "identifier": "tiger-team", "id": self.team.id},
+                    ],
+                }
+            ],
+        }
+
     @freeze_time("2023-01-01 00:00:00")
     @patch(
         "sentry.integrations.github.integration.GitHubIntegration.get_codeowner_file",